a segment of DNA containing a set of contiguous genes that code for enzyme and proteins that are metabolically related.

Includes the control elements (DNA segments that control the transcription of the genes) and the structural genes (transcribed sequentially to produces polygenic mRNA molecule containing coding sequences for all the proteins of the operon) = coordinate expression.

True/False

All genes of a genome are not expressed simultaneiously.

Describe and give examples of a catabolic operon

Encodes enzymes that metabolize a given nutrient, but is only available when that nutrient is present in the body= enyzme induction. Its normal state is "off". The enzymes that are synthesized in response to their substrates are said to be Induced.

Examples:

• gal operon  - converts galactose to glucose
• lac operon - converts lactose to glucose
• ara operon - converts arabinose to glycolitic intermediate

galactose, lactose, arabinose = inducers

codes for enzymes that synthesize a particular nutrient. The presence of that nutrient in the body represses the operon. The default state of the operon is "on"

Examples: Tryptophan (Trp) operon

also amino acids, nucleotides, and cofactors =corepressors

Promoter: region where RNA polymerase binds to initate transcription. Lies upstream of the first transcribed base. On both catablic and anabolic operons.

Operator: Binding site for the repressor protein. Prevents transcription by blocking RNA polymerase. Usually lies between or overlaps the promoter region and first transcribed gene. found in Catabolic & anabolic. Is palindromic.

Regulatory gene: Separate from, but close to operon. Regulates transcription of other genes by coding for the mRNA of the repressor protein that binds to the operator. Has its own promoter.

cAMP Receptor Protein (CRP) or Catabolite Activator protein (CAP) binding site: site that binds the cAMP-bound receptor protein, which activates transcription by RNA polymerase. Usually lies adjacent to promoter. Found only in catabolic. Has some symmetry

Attenuator: DNA region that is usually transcribed and translated. The binding of a ribosomal unit for translation of this site may cause termination of transcription before RNA polymerase reaches the first structural gene. Found in some anabolic operons that code for enzymes that synthesize amino acids.

Presence of the lactose (the inducer) causes the induction of the three lac genes (lac Z, Y, and A in that order) = coordinate expression. The promoter, Lac P, is located upstream of Lac Z and a transcription terminator is located slightly downstream of lac A gene.

The lactose transcript is very unstable and has a half-life only 3 minutes. If lactose is no longer present, the operon is shut off and the mRNA transcript is degraded.

Having all three genes on the same transcript means the relative amt of each protein is always the same under varying conditions

Lac I is the regulatory gene that codes for repressor protein. It lies upstream of the other control elements. (it is not obligatory that a regulatory gene be physically close to the gene cluster).

Lac I transcription is not regulated - it is always being transcribed at a low rate that is relatively independent of cell status.

The repressor is made up of four subunits (tetrameric) which allows it to bind more effectively to the operator site. The repressor has strong affinity for operator (Lac O). Each subunit also has a binding site for the inducer. Binding of the inducer (lactose) causes a conformational change in the repressor (or in the operator site itself) that results in the repressor losing affinity for the operator. Thus, the inducer is a negative allosteric modifier of the repressor.

The palindromic sequence of the operator site reflects the symmetry of the repressor protein

In the absence of glucose, enzyme III causes the phosphorylation of adenylate cyclase which converts ATP to cAMP. Increasing cAMP allows it to bind to the CRP. This resulting complex can then bind to the CAP binding site of the promoter. cAMP is a positive allosteric modifier of CAP, causing it to undergo a conformational change that allows it to bind to the CAP-binding site. CAP facilitates the binding of RNA polymerase to the promoter. W/o it, RNA has a much more diffult time binding making transcription less efficient.

CRP proteins has a helix-turn-helix motif

The Trp operon is an anabolic operon that contains five genes that code for the subunits of the 3 enzymes needed in tryptophan synthesis.

The Trp R gene = regulatory gene that codes for the repressor (tryptophan itself is the COrepressor). THe regulatory gene is not close to the gene cluster.

Active Trp operon is said to be "derepressed"

The repressor is tetrameric (like Lac repressor), about 20 molecules are present per cell. The repressor must be complexed with tryptophan in order to bind to the operator. Hence, tryptophan is a positive allosteric modifier of the repressor (unlike lac repressor and lactose).

The attenuator site lies within the 162 nucleotides b/t the promoter, Trp P, and the Trp E gene.

1. core promoter sequence
2. Proximal promoter sequence
3. Enhancer/silencer/inducer
4. Response element sequence

member of BORIS+CTCF gene family that encodes a transcriptional regulatory protein with 11 highly conserved zinc finger (zf) domains. It can use different combos of zince fingers to bind different DNA target sequences and proteins. It can bind a Histone-acetyltransferase (HAT)-containing complex (transcriptional activator) or it can bind a Histone-deacetylase (HDAC)-containing complex (transcriptional repressor). If the protein binds to an insulator it can block communication b/t enhancers and upstream promoters.

Mutations of this gene has been associated with breast cancer, prostate cancer,and Wilms' Tumor.

TATA box is the considered the core promoter sequence. It lies ~25 bps upstream of the coding gene. It binds the TATA box-binding protein, which bends DNA thru 80 degrees and the AT sequence facilitates unwinding of the molecule.

The site also binds transcription factor II D.

Genomic or parental imprinting is the inherited difference in the expression of a gene depending on whether it is inherited from the mother or father.

Insulin-like growth factor 2 from the father codes for an antisense RNA that blocks synthesis of the mRNA. In the mother, the upstream promoter unmethylated and active (producing a sense RNA) and the downstream promoter is methylated (inactive). In the father the upstream promoter is methylated (inactive) and the downstream is unmethylated (inactive) and codes for the antisense RNA.

Inheritance of 2 copies of the mother genes and none from the father can lead to serious developomental defects.

Most accidental inheritance of 2 copies from one parent are usually fatal.

siRNA genes are about 70bps long and have inverted sequences that can produce double stranded hairpin RNA. A specific enzyme (called Dicer in Drosophila) cuts the ds RNA into small fragments (21-25bps), called small interfering RNA. The siRNAs bind to RNA-induced silencing complex and activates it upon unwinding. The RISC contains an enzyme (called Slicer in Drosophila) that cleaves the mRNA transcript, thus halting gene expression.

Human cells can physiologically silence HIV-1 RNA

They function in cell growth/apoptosis, development, neuronal plasticity, remodeling and insulin secretion.

Overabundance of miRNAs has been implicated in Fragile X Mental Retardation. Up and downregulation of miRNAs has also been implicated in cancer.

Normal gene product pauses cell cycle at G1/S checkpoint. Product of P53 induces transcription of p21, which blocks phophorylation of the G1 cyclin/Cdk2 complex. Allows repair of DNA. If DNA is unable to be repaired the cell undergoes apoptosis.

Mutation of the p53 gene allows the cell to replicate the defective genome.

Overexpression of other gene factor (such as Mdm2 -induced by p53) can prevent p53 interaction with the intiation complex.

p53 mutation occurs in 50% of human tumors, making it the most frequently altered gene found in human cancer.